Fraud in Afghanistan's presidential election may have compromised as many as one in five ballots, a UN official warned today , compounding fears that ballot-stuffing, intimidation and other irregularities could have a decisive impact on the vote.

Afghanistan's election commission sought to play down fears that vote-rigging in the country's presidential election would decide the outcome of the contest.

But concerns were mounting that electoral fraud in the south and east of the country, where few election monitors dared to tread, could help push the number of votes cast for the president, Hamid Karzai, over 50%, handing him victory without the need for a second-round contest. Partial results are expected to be announced later.

One UN official predicted that anywhere between 10% and 20% of the votes cast were illegal, and that negotiations would have to be made to "massage down" Karzai's victory margin. Independent election monitors said almost 700 complaints had been received, around 50 of which were earmarked for immediate investigation because of the risk they could change the outcome.

But the Independent Electoral Commission (IEC), which will publish a small portion of the results tomorrow, said the reported cases of fraud "could not affect the result of the election".

"We have reached the conclusion that 35 cases of reported fraud and violations is not widespread, given the number of polling centres is 6,300," said Zekria Barakzai, the IEC deputy head. "Whoever makes claims that there is widespread fraud should show evidence."

A separate body, the Electoral Complaints Commission, said a steady flow of official complaints had been received. Among a list of 38 complaints lodged by Ashraf Ghani, the former finance minister, were claims that people were forced to vote for the former foreign minister Abdullah Abdullah at gunpoint in the northern province of Balkhm, and of ballot box-stuffing in the western city of Herat.

The ECC, which is run by a board made up mainly of foreigners, has wide-ranging powers to cancel the results from individual polling stations where fraud has been detected.

However Ramazan Bashardost, one of the leading presidential candidates, believes the requirement for good quality evidence in areas where it may be hard to collect reliable eyewitness details will make it extremely difficult to discount large numbers of votes.

Mirwais Yaseni, the deputy speaker of Afghanistan's lower house of parliament, and a presidential candidate, claims thousands of votes cast for him where removed from ballot boxes and earmarked for destruction before being discovered by his supporters. He said the only option available was to "abolish the election".

"They have stolen it already. They are doing it electronically – it is just a matter of picking a number. At first, they were saying it would be 90% for Karzai, but now they are trying to bring it back down to 60%."

Another option would be to offer Abdullah Abdullah, the second-place candidate, who claims Mr Karzai has "rigged" the election, a power-sharing deal. Dr Abdullah was made such offers in the run-up to the election, however, and turned them down.